A man awakens to find he's been altered into a half machine by mysterious doctors. He escapes and finds 8 others like him who band together to fight the evil organization responsible for this inhuman act against them.
Nine people are tricked and forced by a evil organisation called The Neo-Black Ghosts into becoming cyborgs. But they refuse to become the neo-black ghosts killing machines, and guided by Dr. Gilmore the cyborgs escape. They team up in order to fight the neo-black ghosts and injustice where ever it shows it's face.
The cyborgs are no longer in duty, they live normal lives until a misterious space ship lands on earth, the only survivor on the ship warns about an evil conqueror called Zoa that wants to conquer the universe, the cyborgs are back in action..
Cyborg 009 is a story about nine experimental cyborgs (eight male and one female), which have been collected by the evil terrorist group, Black Ghost. Those nine cyborgs with the aid of a scientist turn against Black Ghost's control. Black Ghost in turn starts sending more cyborgs to destroy their first nine experimental cyborgs and causing destruction all around the world.
27 years have passed since the last mission of the Cyborgs and the world seems to have forgotten them by now, but the missile attacks on the metropolis of Shanghai, the scene with which the film opens, awaken fear and the nine Cyborgs are recalled for what could be the their most dangerous and fundamental mission, to find out how and by whom these attacks were launched.
After discovering the existence of demons in Tokyo, the original Cyborg crew led by Dr. Gilmore find themselves in conflict with Devilman, a strong demon believed to be in league with the war-profiteering terrorist organisation, Black Ghost. Meanwhile, a bigger threat emerges when Dr. Adams, a Black Ghost scientist unleashes his new line of high teen Cyborg models against 009 and his friends.
The story depicts Shimamura Joe and the other cyborgs' struggle with the Bresudo, a group of people who possess superhuman powers and intellect, and have manipulated human history since ancient times.